Edward, It looks like the digits are stripped from the element name in generic_fns/structure/internal.py, so it should be 'CH' and not 'CH2' in the table. Could you please update the file?
Thank you, Vitaly On Fri, Dec 17, 2010 at 13:08, V.V. <[email protected]> wrote: > Thank you very much, Edward! > > Vitaly > > > On Fri, Dec 17, 2010 at 13:03, Edward d'Auvergne <[email protected]> wrote: >> Thank you for the detailed message and creating the bug report. This >> is now fixed. Cheers. If you would like the changes without waiting >> for a new release of relax, the new code can be checked out from the >> repository by typing: >> >> $ svn co svn://svn.gna.org/svn/relax/1.3 relax-1.3 >> >> or if this doesn't work: >> >> $ svn co http://svn.gna.org/svn/relax/1.3 relax-1.3 >> >> If you already have a checked out copy, try typing: >> >> $ svn up >> >> This requires installation of the subversion program >> (http://subversion.tigris.org/). >> >> Regards, >> >> Edward >> >> >> On 17 December 2010 19:52, V.V. <[email protected]> wrote: >>> Thank you, Edward! >>> I have submitted the bug report (#17343). Yes, the atom name in the >>> pdb file is labeled "CH2". >>> >>> Vitaly >>> >>> >>> >>> On Fri, Dec 17, 2010 at 11:38, Edward d'Auvergne <[email protected]> >>> wrote: >>>> Hi Vitaly, >>>> >>>> Thank you for identifying this problem. I just had a question, is the >>>> atom named 'CH2' within the PDB file? If you don't mind, would you be >>>> able to create a bug report for this? This would be much appreciated >>>> as it would help other relax users who encounter the same problem as >>>> you have found. This is not too important as it is a missing feature >>>> rather than a bug but, if you could, the bug report submission page is >>>> https://gna.org/bugs/?func=additem&group=relax. >>>> >>>> Thanks, >>>> >>>> Edward >>>> >>>> >>>> >>>> On 15 December 2010 02:51, V.V. <[email protected]> wrote: >>>>> Hello, >>>>> >>>>> I am trying to create a diffusion tensor from the results file, and I >>>>> am running into a following problem after >>>>> "structure.create_diff_tensor_pdb" is invoked: >>>>> >>>>> ================ >>>>> relax> structure.create_diff_tensor_pdb(scale=1.7999999999999999e-06, >>>>> file='tensor.pdb', dir=None, force=True) >>>>> Adding molecule 'diff_tensor' to model None (from the original >>>>> molecule number None of model None) >>>>> >>>>> Chain A >>>>> >>>>> Calculating the centre of mass. >>>>> RelaxWarning: Skipping the atom '#ave_mol1:2...@30' as the element name >>>>> does not exist in the PDB file. >>>>> ================ >>>>> >>>>> In the "results" file, element 30 in the atom name list is 'CH2' (Trp >>>>> side chain). Also if I read the structure file with >>>>> "structure.read_pdb", for each of the Trp residues I get: >>>>> >>>>> ================ >>>>> RelaxWarning: Cannot determine the element associated with atom 'CH2'. >>>>> ================ >>>>> >>>>> It looks like this atom was left out >>>>> (http://www.mail-archive.com/[email protected]/msg06219.html). >>>>> Also, if possible, could you append "OT" atom name (XPLOR format) to >>>>> the oxygen list? >>>>> >>>>> Thank you, >>>>> Vitaly >>>>> >>>>> _______________________________________________ >>>>> relax (http://nmr-relax.com) >>>>> >>>>> This is the relax-users mailing list >>>>> [email protected] >>>>> >>>>> To unsubscribe from this list, get a password >>>>> reminder, or change your subscription options, >>>>> visit the list information page at >>>>> https://mail.gna.org/listinfo/relax-users >>>>> >>>> >>> >> > _______________________________________________ relax (http://nmr-relax.com) This is the relax-users mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users
